In Star Trek: Voyager, episode 23 of season 4 (remember), the episode begins with a civilization unknown until now. They claim to hold the ruins of the USS Voyager, which has otherwise contributed to the history of this civilization in a negative way, whereby Captain Janeway formed an alliance with the enemies of the people in question.
In the historical reconstructions of this event, we see many parts belonging to the ship, such as the Doctor.
This one -- having been deactivated during all these years -- still seems to be several centuries ago. The Doctor is therefore considered as the last "living" witnesses of this war.
The USS Voyager was considered a heavily armed warship with a restless and violent crew. The Doctor has done everything to set the truth about that time, and finally, all ends well, history is approved.
However, what is really going on? In the other episodes, the Doctor is always present, as well as the crew members, and the USS Voyager. At the end of the series, they all return to Earth.
What about this episode that seems to be out of the scope of the story?
I couldn't find any explanation about this episode, except that we could consider it as a separate story, but it doesn't really make sense to put an episode that has nothing to do with it in the middle of the series (even if it's very good and fits in pretty well).
I don't think this question is a duplication of this post, because this one is about the whole episode, as well as what really happened to the crew.